Comparative Genomics and Transcriptional Analysis of Flavobacterium columnare Strain ATCC 49512

Abstract

Flavobacterium columnare is a Gram-negative fish pathogen causing columnaris disease in wild and cultured fish species. Although the pathogen is widespread in aquatic environments and fish worldwide, little is known about biology of F. columnare and mechanisms of columnaris disease pathogenesis. Previously we presented the complete genome sequence of F. columnare strain ATCC 49512. Here we present a comparison of the strain ATCC 49512 genome to four other Flavobacterium genomes. In this analysis, we identified predicted proteins whose functions indicate F. columnare is capable of denitrification, which would enable anaerobic growth in aquatic pond sediments. Anaerobic growth of F. columnare ATCC 49512 with nitrate supplementation was detected experimentally. F. columnare ATCC 49512 had a relatively high number of insertion sequences and genomic islands compared to the other Flavobacterium species, suggesting a larger degree of horizontal gene exchange and genome plasticity. A type VI subtype III secretion system was encoded in F. columnare along with F. johnsoniae and F. branchiophilum. RNA sequencing proved to be a valuable technique to improve annotation quality; 41 novel protein coding regions were identified, 16 of which had a non-traditional start site (TTG, GTG, and CTT). Candidate small noncoding RNAs were also identified. Our results improve our understanding of F. columnare ATCC 49512 biology, and our results support the use of RNA sequencing to improve annotation of bacterial genomes, particularly for type strains.

The Type IX Secretion System Is Required for Virulence of the Fish Pathogen Flavobacterium columnare

“…Further, recent comparative analyses identified all of the T9SS genes in the genomes of each of nine F. columnare strains examined (41,42). For all members of the phylum Bacteroidetes that have the T9SS genes, gldK, gldL, gldM, and gldN are invariably located together in this order as an operon (20,21).…”

“…The action of the gliding motor on SprB proteins that are attached to the substratum results in gliding motility. F. columnare has an SprB ortholog that is thought to be involved in gliding (42). Not surprisingly, deletion of the core F. columnare T9SS gene gldN resulted not only in secretion defects but also in a loss of motility.…”

Complete genome sequence analysis of the fish pathogen Flavobacterium columnare provides insights into antibiotic resistance and pathogenicity related genes

“…The 6-phosphofructokinase 1 (Pf1_00390) and pyruvate kinase (Pf1_01219) are two important enzymes which can regulate the rate of reaction in glycolysis. Moreover, compared genomic analysis showed that some carbohydrate metabolism components and pathways are unique, such as starch and sucrose utilization pathways are present only in F. johnsoniae and F. branchiophilum [16]. Diversity pathways of amino acids biosynthesis and metabolism reflect a highly selfsufficient and unique style in utilizing nutrients.…”

“…Totally 70 genes in nitrogen metabolism pathways were presented, including glycine, serine and threonine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, valine, leucine and isoleucine degradation, alanine, aspartate and glutamate metabolism, arginine and proline metabolism, and histidine metabolism. Genome analysis of F. columnare ATCC 49512 indicated it is capable of denitrification, which would enable anaerobic growth in aquatic pond sediments [16]. After the amino acid degradation, all the nitrogen was excreted in the form of putrescine and NH 3 .…”

“…F. columnare has been classified into three genomovars, in accordance with differences in 16S rRNA sequences and restriction fragment length polymorphism (RFLP) of the 16Se23S rDNA spacer [12e15]. Five complete genome of F. columnare strains were presented [16e19] and comparative genomic analysis were conducted between Flavobacterium, revealing F. columnare is capable of denitrification, which would enable anaerobic growth in aquatic pond sediments [16]. However, the systematical researches of pathogenesis and antibiotic resistance mechanisms of F. columnare are unavailable.…”